After Alex is imprisoned in the Magic Guild and released, exiting the Guild and reentering will cause at least half of the NPCs to disappear (most of the students and guards). I also found, the hard and tedious way, that they are missing after finishing the Crystal Tower, even if one goes straight to the Tower after being released by Mia and goes through the Tower without exiting it at any time. Rather miffed, as there's dialogue I'm missing. I figured the NPCs being missing before going through the Tower was from some load issue, but I really wasn't expecting it to still be the case after finishing the dungeon.

Subtitles for the cutscene at the top also have "innocence" when it should be "innocents." Heh.

Well, so far it looks like only the stuff in the Magic Guild is missing. And the one student who is still there is the one who has Mia's Bromide 4. I'll be interested to see if the NPCs are back after fighting the Crustacean.